NAME
Webservice::InterMine - modules for interacting with InterMine
datawarehouse webservices
SYNOPSIS
use Webservice::InterMine;
my $service = get_service($url, $user, $pass);
my $template = $service->template($name);
my $results = $template->results_with(valueA => 'x', valueB => 'y');
OR:
use Webservice::InterMine 'flymine', 'SOMETOKEN';
my $results = new_query(class => 'Gene')
->select('symbol', 'primaryIdentifier', 'pathways.*')
->where(symbol => [qw/H bib eve zen/])
->all();
OR:
use Webservice::InterMine 'flymine', 'SOMETOKEN', ':no-import';
my $results = Webservice::InterMine->new_query(class => 'Gene')
->select('symbol', 'primaryIdentifier', 'pathways.*')
->where(symbol => [qw/H bib eve zen/])
->all();
OR:
use WebService::InterMine 'flymine';
my $query = load_query(source_file => "my_query.xml");
while (my $result = ) {
process($result);
}
DESCRIPTION
This distribution is the client interface to any implementation of the
InterMine Datawarehousing WebService (www.intermine.org). Primarily used
for biological genomic databases, the webservice allows the user to
easily write and execute structured queries.
This module allows you to interact with one or more webservices by
providing a url to an InterMine implementation.
INSTALLATION AND DEPENDENCIES
This package can be installed using the following commands
(Module::Build >= 0.36 is required):
perl Build.PL
./Build test
sudo ./Build install
If any runtime dependencies are missing, you can use the following
command to install them:
sudo ./Build installdeps
IMPORT STATEMENTS
You must import the module with "use" to utilise its functionality.
Additional parameters can be supplied at import to specify a default
service.
Simply import the module:
use Webservice::InterMine;
Import the module, and specify the default service as FlyMine (the url
will be looked up at the central mine registry
.
use Webservice::InterMine 'flymine';
The same, only with the full url, eliminating the need for an extra
lookup:
use Webservice::InterMine 'www.flymine.org/query';
The same, but with authentication supplied by an API access token:
use Webservice::InterMine 'flymine', 'SOMETOKEN';
The same, but with authentication supplied username and password
credentials: (deprecated)
use Webservice::InterMine 'flymine', 'username', 'password';
The same, with explicit, named parameters:
use Webservice::InterMine root => 'flymine', user => 'username', pass => 'password';
Calling "use Webservice::InterMine" without any parameters simply means
you need to either specify the webservice url on every call, or call the
methods on a service directly.
If you pass parameters to import, a default service will be set meaning
method calls will not require the webservice url. Unless you are
intending to access multiple services, this form is recommended.
If you do not wish to import the standard functions into your namespace,
instead choosing to call them as class methods, but still wish to set a
default service, you can use the following syntax:
use Webservice::InterMine "flymine", "TOKEN", ':no-import';
Using Queries
The main reason to access the InterMine webservices is to query for
data. The most flexible way to do this is by using Queries:
my $query = resultset("Gene")->select("*", "proteins.*")->where(symbol => [qw/h r eve zen bib/]);
while (my $gene = ) {
print $gene->symbol, map {$_->name} $gene->proteins, "\n";
}
As you can see, queries can be concisely defined, and their results
easily accessed. You can process a query's results all at once, or using
iteration, as in the example above. Iteration is less memory hungry, as
only the current row of data needs to be held in memory at once, which
can be important when dealing with large data sets.
Using Templates
Templates are predefined queries that make running queries easier, as
you don't have to define the logic yourself. Every mine comes with many
predefined searches, and you just have to enter a few parameters:
my $results = $service->template("Gene_Proteins")->results_with(valueA => "eve");
These templates are simple to use, and they have all the power of full
queries as well. You can process results just as powerfully with them.
Using Lists
Lists are saved result sets in a webservice you can access, create,
modify and delete (provided you are logged in):
my $service = Webservice::InterMine->get_service("flymine", "MYTOKEN");
my $list = $service->list("MyAwesomeList");
my $new_list = $service->new_list(content => "some_file.text", type => "Gene");
my $intersection = $list & $new_list;
$intersection->rename("GenesInCommon");
$new_list->delete; # Not actually necessary - it had no name so would have been automatically deleted anyway.
Lists enable you to collect and manage results and lists of items of
interest to you. You can use them in queries, and display their
contents, as well as perforing set-logic operations on them. When you
are done, you can view the lists in the webservice, where you can use
the analysis widgets to assess the data you have processed.
IMPORTS
The following functions are imported into the callers namespace. This
can be prevented by "require"-ing the module instead.
* get_service
* new_query
* resultset
* get_template
* get_list
* new_list
* load_query
METHODS
new_query( [from => \@service_args], [%query_args] )
returns a new query object for you to fill in with constraints before
being run to get its results.
Parameters:
* from => [url, user, pass]
An array ref of arguments to pass to get_service. This information
can be used to specify a different service than the one named on
import, or to specify one when none was named on import.
* %query_args
Key value pairs of arguments to pass to the query constructor in
Webservice::InterMine::Service. This methid serves as sugar for the
factory method in that class.
Please see Webservice::InterMine::Query, Webservice::InterMine::Service.
new_list( %list_args, [from => \@service_args] )
Creates a new list with the content specified by the list arguments. The
"content" key-word parameter will always be required. For a full
specification of creating lists, see: Webservice::InterMine::Service.
Parameters:
* from => [url, user, pass]
An array ref of arguments to pass to get_service. This information
can be used to specify a different service than the one named on
import, or to specify one when none was named on import.
* %list_args
Key value pairs of arguments to pass to the list constructor in
Webservice::InterMine::Service. This methid serves as sugar for the
factory method in that class.
get_list( $list_name, [from => \@service_args] )
Get the list of the given name from the default service, or the given
service if details are supplied.
load_query(source_file|source_string => $source, %opts, [from => [\@service_args]])
Returns a query object based on xml you have previously saved, either as
a string or as a file. For a file pass:
load_query(source_file => $file);
For a string:
load_query(source_string => $string);
If you want a specific service, call it thus:
load_query(from => [$name, $user, $pass], source_string => $string);
OR:
load_query(from => [$name, $user, $pass], source_string => $string);
Please see Webservice::InterMine::Query::Saved
template( $name, [from => \@service_args], [%opts] )
returns the named template (if it exists - if not it returns undef). If
you pass a url, it returns the named template from the specified
webservice.
Please see Webservice::InterMine::Query::Template
get_template
Alias for "template"
saved_query( $name, [from => \@service_args], %options ) NOT IMPLEMENTED YET
returns the named saved_query (if it exists - if not it returns undef).
If you pass a url, it returns the named query from the specified
webservice.
This method requires you to have provided a username and password to the
webservice for authentication.
Please see Webservice::InterMine::Query::Saved
get_service( $root, ($token | $user, $pass) )
returns a webservice object, which is used to construct queries and
fetch templates and saved queries. If a url is passed, the webservice
for that url is returned, otherwise the service for the url given to
"use" is returned.
Get the default service defined at import:
use Webservice::InterMine qw(http://www.intermine.org/intermine-demo SOMETOKEN);
my $service = InterMine::Webservice->get_service;
OR get a specific service, authenticated using an API access token:
my $service = InterMine::Webservice->get_service($url, $token);
Fetch that same authenticated service later:
my $service = InterMine::Webservice->get_service($url);
OR make the same call using a hash reference and named parameters:
my $service = InterMine::Webservice->get_service({
root => $url, token => $token
});
Parameters:
* $root - The base url for the service.
* $token - An API access key
* $username, $password - A user's login credentials
InterMine webservices support two authentication mechanisms to provide
access to private data. The recommended method is to use API access
keys, which have the advantage of eliminating the need to transmit your
login details. If compromised, an access key can be easily changed or
disabled without needing to change either the associated username or
password. However this facility is new, so for backwards compatibility,
the older mechanism for passing along username and password credentials
has been retained.
If three arguments are supplied, they will be interpreted as "($root,
$user, $pass)", but if two are supplied, they will be intepreted as
"($root, $token)".
These arguments may also be passed in a keyword/hash style, either as a
list or a hash reference, in which case the full list will be passed to
the Webservice::InterMine::Service::new constructor.
If a service for a url has been created previously, that one is
returned, even if different login details are provided.
Please see: Webservice::InterMine::Service
clean_temp_lists()
Deletes all automatically created anonymous lists. Any renamed lists
will be spared the clean-up. This method is called on system exit,
unless the variable $Webservice::InterMine::CLEAN_UP is set to a false
value.
get_{minename}(user, pass)
An unknown method preceded with 'get_' will be interpreted as a mine
name, and an attempt will be made to return a service with that name.
SEE ALSO
* Webservice::InterMine::Cookbook for a guide on how to use these
modules.
* Webservice::InterMine::Query
* Webservice::InterMine::Service
* Webservice::InterMine::List
* Webservice::InterMine::Query::Template
* Webservice::InterMine::Query::Saved
* Webservice::InterMine::Bio Biologically specific roles.
AUTHOR
Alex Kalderimis ""
BUGS
Please report any bugs or feature requests to "dev@intermine.org".
SUPPORT
You can find documentation for this module with the perldoc command.
perldoc Webservice::InterMine
You can also look for information at:
* InterMine
* Documentation
COPYRIGHT AND LICENSE
Copyright 2006 - 2011 FlyMine, all rights reserved.
This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.